galE2 Family assigned · medium auto-curated
H37Rv Rv0501 · MTBC0 mtbc0_000529 ·
376 aa · 594995–596125 (+) ·
RefSeq NP_215050.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | UDP-glucose 4-epimerase GalE |
|---|---|
| MTBC0 PGAP re-annotation | SDR family oxidoreductase |
| Revised (this work) | SDR family oxidoreductase. Pfam: Epimerase (PF01370.28), GDP_Man_Dehyd (PF16363.12), 3Beta_HSD (PF01073.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKT3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0501 |
UniProt still lists this protein as Uncharacterized protein Rv0501; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolismM Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | galE2 |
| eggNOG description | epimerase dehydratase |
| Orthologous group | COG0451 |
| EC number |
EC 5.1.3.2
|
| KEGG orthology |
K01784
|
| KEGG pathways |
map00052, map00520, map01100
|
| KEGG modules |
M00361, M00362, M00632
|
| Gene Ontology (12) |
GO:0005575, GO:0005576, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0044424, GO:0044444, GO:0044464, GO:0071944
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.233 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 2 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Epimerase | PF01370.28 | 2.7e-22 | 26–256 | NAD dependent epimerase/dehydratase family |
GDP_Man_Dehyd | PF16363.12 | 2.4e-12 | 27–160 | GDP-mannose 4,6 dehydratase |
3Beta_HSD | PF01073.26 | 1.9e-09 | 27–155 | 3-beta hydroxysteroid dehydrogenase/isomerase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0500B (Rv0500B, len: 33 aa. Conserved hypothetical protein. Basic protein 18 of the 33 aa are Arg or Lys, with strong similarity to AL079345|SCE68_), high confidence from genomic context alone (score 790 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0502 hyp |
hypothetical protein | 970 | 970 ctx | neighborhood:882 cooccurence:742 |
Rv0322 udgA |
UDP-glucose 6-dehydrogenase UdgA | 950 | 948 | coexpression:414 database:900 |
Rv3809c glf |
UDP-galactopyranose mutase | 969 | 928 | database:900 textmining:589 |
Rv3634c galE1 |
UDP-glucose 4-epimerase | 920 | 921 | database:900 |
Rv3468c |
dTDP-glucose 4,6-dehydratase | 916 | 917 | database:900 |
Rv0993 galU |
UTP--glucose-1-phosphate uridylyltransferase | 910 | 905 | database:900 |
Rv0618 galTa |
Rv0618, (MTCY19H5.03c), len: 231 aa (probable partial CDS). Probable galTa, first part of galactose-1-phosphate uridylyltransferase, highly | 907 | 903 | database:900 |
Rv0705 rpsS |
30S ribosomal protein S19 | 819 | 819 | experimental:463 database:574 |
Rv0682 rpsL |
30S ribosomal protein S12 | 816 | 808 | experimental:463 database:573 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 805 | 799 | experimental:463 database:578 |
Rv0707 rpsC |
30S ribosomal protein S3 | 804 | 797 | experimental:463 database:578 |
Rv0721 rpsE |
30S ribosomal protein S5 | 802 | 795 | experimental:463 database:575 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 790 | 791 | experimental:436 database:548 |
Rv0500B |
Rv0500B, len: 33 aa. Conserved hypothetical protein. Basic protein 18 of the 33 aa are Arg or Lys, with strong similarity to AL079345|SCE68_ | 789 | 790 ctx | neighborhood:787 |
Rv2056c rpsN2 |
30S ribosomal protein S14 | 789 | 790 | experimental:436 database:548 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: UDP-glucose 4-epimerase GalE
- MTBC0 PGAP product: SDR family oxidoreductase
- Pfam (hmmscan --cut_ga): Epimerase PF01370.28 (E=3e-22), GDP_Man_Dehyd PF16363.12 (E=2e-12), 3Beta_HSD PF01073.26 (E=2e-09)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215050.2)
- Domains: Pfam-A via hmmscan --cut_ga — Epimerase (PF01370.28), GDP_Man_Dehyd (PF16363.12), 3Beta_HSD (PF01073.26)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0451 - Curated reference: UniProt P9WKT3 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
99 functional partner(s); context anchor
Rv0500B - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000529|Rv0501|galE2 MSSSNGRGGAGGVGGSSEHPQYPKVVLVTGACRFLGGYLTARLAQNPLINRVIAVDAIAPSKDMLRRMGRAEFVRADIRNPFIAKVIRNGEVDTVVHAAAASYAPRSGGSAALKELNVMGAMQLFAACQKAPSVRRVVLKSTSEVYGSSPHDPVMFTEDSSSRRPFSQGFPKDSLDIEGYVRALGRRRPDIAVTILRLANMIGPAMDTTLSRYLAGPLVPTIFGRDARLQLLHEQDALGALERAAMAGKAGTFNIGADGILMLSQAIRRAGRIPVPVPGFGVWALDSLRRANHYTELNREQFAYLSYGRVMDTTRMRVELGYQPKWTTVEAFDDYFRGRGLTPIIDPHRVRSWEGRAVGLAQRWGSRNPIPWSGLR